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- PDB-4das: Crystal structure of Bullfrog M ferritin -

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Basic information

Entry
Database: PDB / ID: 4das
TitleCrystal structure of Bullfrog M ferritin
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / iron storage protein / 24-subunit maxiferritin / four-helix bundle subunit / ferroxidase
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Ferritin, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsBertini, I. / Lalli, D. / Mangani, S. / Pozzi, C. / Rosa, C. / Turano, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural insights into the ferroxidase site of ferritins from higher eukaryotes.
Authors: Bertini, I. / Lalli, D. / Mangani, S. / Pozzi, C. / Rosa, C. / Theil, E.C. / Turano, P.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, middle subunit
B: Ferritin, middle subunit
C: Ferritin, middle subunit
D: Ferritin, middle subunit
E: Ferritin, middle subunit
F: Ferritin, middle subunit
G: Ferritin, middle subunit
H: Ferritin, middle subunit
I: Ferritin, middle subunit
J: Ferritin, middle subunit
K: Ferritin, middle subunit
L: Ferritin, middle subunit
M: Ferritin, middle subunit
N: Ferritin, middle subunit
O: Ferritin, middle subunit
P: Ferritin, middle subunit
Q: Ferritin, middle subunit
R: Ferritin, middle subunit
S: Ferritin, middle subunit
T: Ferritin, middle subunit
U: Ferritin, middle subunit
V: Ferritin, middle subunit
X: Ferritin, middle subunit
W: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,00558
Polymers494,95624
Non-polymers4,04934
Water27,4731525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area105120 Å2
ΔGint-224 kcal/mol
Surface area134490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.951, 210.951, 323.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ...
Ferritin, middle subunit / / Ferritin M / Ferritin H' / Ferritin X


Mass: 20623.182 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07798, ferroxidase
#2: Chemical...
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1525 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.0 M sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2009 / Details: Toroidal Mirror
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.56→100.5 Å / Num. all: 259578 / Num. obs: 259578 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 42.386 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 5.2
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 1.7 / Num. unique all: 37996 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MFR

1mfr


Resolution: 2.56→79.51 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.278 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.288 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23895 13045 5 %RANDOM
Rwork0.186 ---
all0.18867 246309 --
obs0.18867 246309 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.184 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.56→79.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34042 0 268 1525 35835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02134948
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.95346868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74554110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44624.7291958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.266156456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.96315216
X-RAY DIFFRACTIONr_chiral_restr0.1160.24902
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226648
X-RAY DIFFRACTIONr_mcbond_it0.6971.520550
X-RAY DIFFRACTIONr_mcangle_it1.468232899
X-RAY DIFFRACTIONr_scbond_it2.689314398
X-RAY DIFFRACTIONr_scangle_it4.6554.513969
LS refinement shellResolution: 2.56→2.626 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 966 -
Rwork0.291 18209 -
obs-18209 98.19 %

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